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PubMed1991

A highly conserved nucleotide string shared by all genomes of human papillomaviruses.

The nucleotide string TAAAACGAAAGT is the longest perfect homology shared by all sequenced human papillomavirus genomes. This nucleotide string, which was also found to be highly specific for human papillomavirus genomes, shares the same genomic position in all viral types (5' end of the E1 open reading frame) and putatively codes in every case for the same amino acids. One possible evolutionary model was used to estimate the probability of random occurrence of the nucleotide string in 10 human papillomavirus genomes. It assumed that the universal string had been subjected to the same mutation rate as the entire E1 open reading frame. The estimated probability was found to be very low, suggesting that the conservation of the string could not have resulted from random divergence and that its conservation among human papillomaviruses is likely to reflect the occurrence of biological constraints. It is speculated that this nucleotide string may be required to code for amino acids indispensable for the nuclear localization of E1-coded peptides or to bind cellular factors affecting viral replicative functions. Definitive evidence is expected to come from oligonucleotide-protein binding experiments and from site-directed mutagenesis of cloned HPV genomes. This motif, universal among human papillomaviruses, is being successfully used in the design of consensus primers from the early region.

Amino Acid Sequence↗

PubMed2005

Prospective randomised clinical trial of single versus double purse-string stapled mucosectomy in the treatment of prolapsed haemorrhoids.

BACKGROUND AND AIMS: Despite the excellent results published on circular stapled mucosectomy (CSM), there is still some concern about the application of PPH-33 in the advanced haemorrhoidal disease, where a major prolapse may lead to insufficient resection and ensuing early recurrence. This study is aimed at comparing the outcomes after single purse-string CSM versus double purse-string CSM. PATIENTS AND METHODS: A prospective randomised clinical trial of single versus double purse-string CSM for grade III-IV symptomatic haemorrhoids was used. One hundred consecutive patients were randomised to single (group 1, N=50) versus double purse-string CSM (group 2, N=50). RESULTS: The mean age was 50.7 years, with a predominance of males (63 vs. 37). Haemorrhoids were classified as grade III in 59% and grade IV in 41% of the patients. Mean follow-up was 26 months. Demographic and clinical features showed no differences between the two groups. The size of the resected doughnut was greater in group 2 (4.95 vs. 3.55 cm; p<0.05), as was the distance of the suture from the dentate line (3.56 vs. 3.16 cm; p<0.05). Early postoperative pain was significantly less in group 2 (linear analogue scale from 0 to 10), 2.08 vs. 3.56 (p<0.001). Postoperative haemorrhage was absent or minimal in 79% of patients. Three patients from group 1 reported persistent pain that was resolved within the first few postoperative months. There were two recurrences in group 1. CONCLUSION: Double purse-string CSM resects a greater doughnut, increases the distance of the staple suture from the dentate line and reduces early postoperative pain in comparison to single purse-string CSM. Larger series are necessary to assert whether recurrence is lower.

Adult↗

PubMed1995

The nucleotide and deduced amino acid sequence of a rat cysteine string protein.

Cysteine string proteins are novel, heavily lipidated components of synaptic vesicles. They have previously been studied in Drosophila (insect) and Torpedo (fish). To facilitate further investigation of the structure and function of these proteins in mammals, we isolated and sequenced the cDNA and conducted an initial characterization of a rat cysteine string protein. Nucleotide sequencing reveals that this rat protein is highly homologous to the insect and fish cysteine string proteins. At the amino acid level, the fish and rat proteins are 82% identical. The rat cysteine string protein is encoded by an approximately 5 kb mRNA that is ubiquitously expressed in rat brain. Using antibodies that cross-react with the rat protein, we find that the rat cysteine string protein is predominantly associated with nerve endings and synaptic vesicles. Moreover, like its Torpedo (fish) counterpart, it is extensively fatty acylated. It will be of considerable interest to ascertain the functional correlates of these cross-species similarities of cysteine string proteins.

Amino Acid Sequence↗

PubMed1985

Use of keyed character string data structures and operators in models of primate groups.

Many primate populations exhibit forms of organization that are both complex and highly dynamic. A prototype of a general purpose primate population computer modelling system has been developed; this modelling system provides data structures and operators that facilitate computer representation of many static and dynamic features of primate population organization. In this system, primate group structures are represented by text strings known as key strings. A key string begins with a label or key character that identifies its population element type. The label character is followed by data fields contained between bounds marker characters. Nested key strings can be used to concisely represent many of the structural features of social groups in different primate species. Changes in group structures are accomplished by key string insertion, deletion and move operations. Models of structures and processes in island, rhesus monkey and hamadryas baboon populations built with this prototype modelling system are discussed. In these pilot applications, use of key string data structures and operators greatly simplifies many aspects of model construction.

Animals↗

PubMed2000

Apparent string shortening concomitant with letter crowding.

In our previous studies of the crowding effect, we have observed that human observers tend to underestimate the length of a letter string (the number of letters in the string) when the letters are close to visual acuity, and the interletter spacings are small. In this study, we asked our observers to identify letters in randomly presented four-letter and five-letter strings. We found that, when a priori knowledge of the lengths of letter strings was not available, the probability of underestimating string length increased with decreasing interletter spacing. The causes of underestimation errors appeared to be the omission of an interior letter and the merging of two neighboring letters. Since our experiments were conducted in the foveal region, neither spatial uncertainty nor split attention can explain the underestimation errors. The effect of the point spread function of the eye on closely packed letter strings is discussed.

Adult↗

PubMed1999

Wound-induced assembly and closure of an actomyosin purse string in Xenopus oocytes.

BACKGROUND: Both single cells and multicellular systems rapidly heal physical insults but are thought to do so by distinctly different mechanisms. Wounds in single cells heal by calcium-dependent membrane fusion, whereas multicellular wounds heal by a variety of different mechanisms, including circumferential contraction of an actomyosin 'purse string' that assembles around wound borders and is dependent upon the small GTPase Rho. RESULTS: We investigated healing of puncture wounds made in Xenopus oocytes, a single-cell system. Oocyte wounds rapidly assumed a circular morphology and constricted circumferentially, coincident with the recruitment of filamentous actin (F-actin) and myosin-II to the wound borders. Surprisingly, recruitment of myosin-II to wound borders occurred before that of F-actin. Further, experimental disruption of F-actin prevented healing but did not prevent myosin-II recruitment. Actomyosin purse-string assembly and closure was dependent on Rho GTPases and extracellular calcium. Wounding resulted in reorganization of microtubules into an array similar to that which forms during cytokinesis in Xenopus embryos. Experimental perturbation of oocyte microtubules before wounding inhibited actomyosin recruitment and wound closure, whereas depolymerization of microtubules after wounding accelerated wound closure. CONCLUSIONS: We conclude the following: actomyosin purse strings can close single-cell wounds; myosin-II is recruited to wound borders independently of F-actin; purse-string assembly is dependent on a Rho GTPase; and purse-string assembly and closure are controlled by microtubules. More generally, the results indicate that actomyosin purse strings have been co-opted through evolution to dispatch a broad variety of single-cell and multicellular processes, including wound healing, cytokinesis and morphogenesis.

Actins↗

PubMed2004

Is there training-dependent reorganization of digit representations in area 3b of string players?

OBJECTIVE: The digit representations in area 3b were studied to examine whether there is training-dependent reorganization in string players. METHODS: Somatosensory evoked magnetic fields were recorded following electrical stimulation of digits 1 (D1), 2 (D2) and 5 (D5) of both hands in 8 string players and of the left hand in 12 control subjects. The N20m and P30m responses, and high-frequency oscillations (HFOs) were separated by 3-300 Hz and 300-900 Hz bandpass filtering. RESULTS: The dipole locations on the coronal plane and strengths of D1, D2 and D5, and D1-D5 cortical distance estimated at the peak of N20m or P30m did not differ between left and right hand in string players or between left hand in string players and controls. On the other hand, the dipole locations of D2 estimated from N20m and P30m and of D1 from N20m were significantly anterior, the D2-D5 distance from P30m longer, and the number of HFO peaks larger for D5 in string players than controls. CONCLUSIONS/SIGNIFICANCE: With strong mutual competition among the fingering digits, the scale of reorganization should be much smaller as compared with the competition-free denervation-induced reorganizations. Taken together, the training-dependent reorganization of somatosensory cortex in string players is manifest not only in the enlarged cortical representation but also in the enhanced HFOs presumably representing activity of the fast-spiking interneurons.

Adolescent↗

PubMed1999

Dynamics of letter string perception in the human occipitotemporal cortex.

The inferior occipitotemporal brain areas, especially in the left hemisphere, have been shown to be involved in the processing of written words and letter strings. This processing probably occurs within 200 ms after presentation of the letter string. It has also been suggested that this activation may differ between fluent and dyslexic readers. Using whole-head magnetoencephalography, we studied the spatiotemporal dynamics of brain processes evoked by visually presented letter strings in 12 healthy adult subjects. Our achromatic stimuli consisted of rectangular patches in which single letters, two-letter syllables, four-letter words, or symbol strings of equal length were embedded and to which variable noise was added. This manipulation dissociated three different response patterns. The first of these patterns took place approximately 100 ms after stimulus onset, originated in areas surrounding the V1 cortex and was distributed along the ventral visual stream, extending laterally as far as V4v. This response was systematically modulated by noise but was insensitive to the stimulus content, suggesting involvement in early visual analysis. The second pattern took place approximately 150 ms after stimulus onset and was concentrated in the inferior occipitotemporal region with left-hemisphere dominance. This activation showed a preference for letter strings, and its strength and timing correlated with the speed at which the subjects were able to read words aloud. The third pattern also occurred in the time window approximately 150 ms after stimulus onset, but originated mainly in the right occipital area. Like the second pattern, it was modulated by string length, but showed no preference for letters compared with symbols. The present data strongly support the special role of the left inferior occipitotemporal cortex in visual word processing within 200 ms after stimulus onset.

Adult↗

PubMed2002

Dynamics of visual feature analysis and object-level processing in face versus letter-string perception.

Neurones in the human inferior occipitotemporal cortex respond to specific categories of images, such as numbers, letters and faces, within 150-200 ms. Here we identify the locus in time when stimulus-specific analysis emerges by comparing the dynamics of face and letter-string perception in the same 10 individuals. An ideal paradigm was provided by our previous study on letter-strings, in which noise-masking of stimuli revealed putative visual feature processing at 100 ms around the occipital midline followed by letter-string-specific activation at 150 ms in the left inferior occipitotemporal cortex. In the present study, noise-masking of cartoon-like faces revealed that the response at 100 ms increased linearly with the visual complexity of the images, a result that was similar for faces and letter-strings. By 150 ms, faces and letter-strings had entered their own stimulus-specific processing routes in the inferior occipitotemporal cortex, with identical timing and large spatial overlap. However, letter-string analysis lateralized to the left hemisphere, whereas face processing occurred more bilaterally or with right-hemisphere preponderance. The inferior occipitotemporal activations at approximately 150 ms, which take place after the visual feature analysis at approximately 100 ms, are likely to represent a general object-level analysis stage that acts as a rapid gateway to higher cognitive processing.

Acoustic Stimulation↗

PubMed2000

Formation of electron strings in narrow band polar semiconductors

We show that linear electron strings may arise in polar semiconductors. A single string consists of M spinless fermions trapped by an extended polarization well of a cigar shape. Inside the string the particles are free although they interact with each other via Coulomb forces. The strings arise as a result of an electronic phase separation associated with an instability of small adiabatic polarons. We have found the length of the string which depends on dielectric constants of semiconductors. The appearance of these electron strings may have an impact on the effect of stripe formation observed in a variety of high- T(c) experiments.

Journal Article↗

PubMed2003

Quantum bit string commitment.

A bit string commitment protocol securely commits N classical bits so that the recipient can extract only M<N bits of information about the string. Classical reasoning suggests that bit string commitment implies bit commitment and hence, given the Mayers-Lo-Chau theorem, that nonrelativistic quantum bit string commitment is impossible. Not so: there exist nonrelativistic quantum bit string commitment protocols, with security parameters epsilon and M, that allow A to commit N=N(M,epsilon) bits to B so that A's probability of successfully cheating when revealing any bit and B's probability of extracting more than N'=N-M bits of information about the N bit string before revelation are both less than epsilon. With a restrictive definition of security against A, N can be taken to be O(exp(CN')) for a positive constant C. I briefly discuss possible applications.

Journal Article↗

PubMed2006

Collisions of strings with Y junctions.

We study the dynamics of Nambu-Goto strings with junctions at which three strings meet. In particular, we exhibit one simple exact solution and examine the process of intercommuting of two straight strings in which they exchange partners but become joined by a third string. We show that there are important kinematical constraints on this process. The exchange cannot occur if the strings meet with very large relative velocity. This may have important implications for the evolution of cosmic superstring networks and non-Abelian string networks.

Journal Article↗

PubMed1994

Purification of an oligo(dG).oligo(dC)-binding sea urchin nuclear protein, suGF1: a family of G-string factors involved in gene regulation during development.

Contiguous deoxyguanosine residues (G strings) have been implicated in regulation of gene expression in several organisms via the binding of G-string factors. Regulation of expression of the chicken adult beta-globin gene may involve the interplay between binding of an erythrocyte-specific G-string factor, BGP1, and the stability of a positioned nucleosome (C. D. Lewis, S. P. Clark, G. Felsenfeld, and H. Gould, Genes Dev. 2:863-873, 1988). We have purified a 59.5-kDa nuclear protein (suGF1) from sea urchin embryos by DNA affinity chromatography. suGF1 has high binding affinity and specificity for oligo(dG).oligo(dC). The identity of the purified protein was confirmed by renaturation of sequence-specific DNA-binding activity from a sodium dodecyl sulfate-polyacrylamide gel slice and by Southwestern (DNA-protein) blotting. suGF1 binds in vitro to a G11 string present in the H1-H4 intergenic region of a sea urchin early histone gene battery. This suGF1 DNA recognition site occurs within a homopurine-homopyrimidine stretch previously shown to be incorporated into a positioned nucleosome core in vitro. DNase I footprinting shows that suGF1 protects the same base pairs on the promoter of the chicken beta A-globin gene as does BGP1. We show that a G-string cis-regulatory element of a sea urchin cell lineage-specific gene LpS1 (M. Xiang, S.-Y. Lu, M. Musso, G. Karsenty, and W. H. Klein, Development 113:1345-1355, 1991) also represents a high-affinity recognition site for suGF1. suGF1 may be a member of a family of G-string factors involved in the regulation of expression of unrelated genes during development of a number of different organisms.

Animals↗

PubMed2004

Neutrophil string formation: hydrodynamic thresholding and cellular deformation during cell collisions.

Neutrophils unexpectedly display flow-enhanced adhesion (hydrodynamic thresholding) to L-selectin in rolling or aggregation assays. We report that the primary collision efficiency (epsilon) of flowing neutrophils with preadhered neutrophils on intercellular adhesion molecule-1 (ICAM-1) or fibrinogen also displayed a maximum of epsilon approximately 0.4-0.45 at a wall shear rate of 100 s(-1), an example of thresholding. Primary collision lifetime with no detectable bonding decreased from 130 to 10 ms as wall shear rate increased from 30 to 300 s(-1), whereas collision lifetimes with bonding decreased from 300 to 100 ms over this shear range using preadhered neutrophils on ICAM-1, with similar results for fibrinogen. Antibodies against L-selectin, but not against CD11a, CD11b, or CD18, reduced epsilon at 100 s(-1) by >85%. High resolution imaging detected large scale deformation of the flowing neutrophil during the collision at 100 s(-1) with the apparent contact area increasing up to approximately 40 microm(2). We observed the formation of long linear string assemblies of neutrophils downstream of neutrophils preadhered to ICAM-1, but not fibrinogen, with a maximum in string formation at 100 s(-1). Secondary capture events to the ICAM-1 or fibrinogen coated surfaces after primary collisions were infrequent and short lived, typically lasting from 500 to 3500 ms. Between 5 and 20% of neutrophil interactions with ICAM-1 substrate converted to firm arrest (>3500 ms) and greatly exceeded that observed for fibrinogen, thus defining the root cause of poor string formation on fibrinogen at all shear rates. Additionally, neutrophils mobilized calcium after incorporation into strings. Static adhesion also caused calcium mobilization, as did the subsequent onset of flow. To our knowledge, this is the first report of 1). hydrodynamic thresholding in neutrophil string formation; 2). string formation on ICAM-1 but not on fibrinogen; 3). large cellular deformation due to collisions at a venous shear rate; and 4), mechanosensing through neutrophil beta(2)-integrin/adhesion. The increased contact area during deformation was likely responsible for the hydrodynamic threshold observed in the primary collision efficiency since no increase in primary collision lifetime was detected as shear forces were increased (for either surface coating).

CD11a Antigen↗

PubMed1999

Spontaneous recanalization of postoperative severe graft stenosis. What is the cause and prognosis of the "string sign" in the internal thoracic artery?

A 68-year-old female with unstable angina was treated surgically. She was referred to the surgical ward by cardiologists because of a diagnosis of unstable angina with three vessel disease. On a coronary angiogram (CAG), 90% stenoses were found in the left anterior descending coronary artery (LAD), circumflex (CX), and right coronary artery (RCA). She received elective coronary artery bypass grafting (CABG), in which the left internal thoracic artery (LITA) was anastomosed to the LAD and reversed saphenous vein grafts (SVG) were made to segment 12 of the CX, and segment 4PD of the RCA, respectively. The postoperative course was uneventful, but postoperative early graftgraphy revealed distal narrowing of the LITA graft as the so-called "string sign". However, one year post surgery, the LITA string sign was not found and its patency had markedly improved on the second graftgram. It is reported that the LITA "string sign" might cause late graft occlusion. However, this LITA graft evidently enlarged the size and increased the flow of the artery in proportion to myocardial blood demand. To our knowledge, it has not been reported that an in situ LITA string sign on postoperative early graftgram has disappeared in the late phase. We hypothesize that the LITA string sign might be caused by several different factors such as flow competition, spasm, and/or technical problems. In any event, the LITA string sign does not cause graft occlusion in the late postoperative period in every case.

Aged↗

PubMed2001

Evaluating UMLS strings for natural language processing.

The National Library of Medicine's Unified Medical Language System (UMLS) is a rich source of knowledge in the biomedical domain. The UMLS is used for research and development in a range of different applications, including natural language processing (NLP). In this paper we investigate the nature of the strings found in the UMLS Metathesaurus and evaluate them for their usefulness in NLP. We begin by identifying a number of properties that might allow us to predict the likelihood of a given string being found or not found in a corpus. We use a statistical model to test these predictors against our corpus, which is derived from the MEDLINE database. For one set of properties the model correctly predicted 77% of the strings that do not belong to the corpus, and 85% of the strings that do belong to the corpus. For another set of properties the model correctly predicted 96% of the strings that do not belong to the corpus and 29% of the strings that do belong to the corpus.

MEDLINE↗

PubMed2002

A string pattern regression algorithm and its application to pattern discovery in long introns.

We present a new approach to pattern discovery called string pattern regression, where we are given a data set that consists of a string attribute and an objective numerical attribute. The problem is to find the best string pattern that divides the data set in such a way that the distribution of the numerical attribute values of the set for which the pattern matches the string attribute, is most distinct, with respect to some appropriate measure, from the distribution of the numerical attribute values of the set for which the pattern does not match the string attribute. By solving this problem, we are able to discover, at the same time, a subset of the data whose objective numerical attributes are significantly different from rest of the data, as well as the splitting rule in the form of a string pattern that is conserved in the subset. Although the problem can be solved in linear time for the substring pattern class, the problem is NP-hard in the general case (i.e. more complex patterns), and we present an exact but efficient branch-and-bound algorithm which is applicable to various pattern classes. We apply our algorithm to intron sequences of human, mouse, fly, and zebrafish, and show the practicality of our approach and algorithm. We also discuss possible extensions of our algorithm, as well as promising applications, such as microarray gene expression data.

Algorithms↗

PubMed1989

[A new technic for esophago-enteral anastomosis with a mechanical stapler without purse-string sutures].

Staplers have improved the results of esophageal surgery, in our experience and in others experience, as esophago-enteric anastomoses have become safer and faster than when manual suturing is used. Probably one of the last problems in the stapler technique, especially in the thoracic area, is the performance of on adequate esophageal purse-string suture: an improper performance of this suture can cause a dangerous leak of the anastomosis. So, many surgeons, to reduce the risk of esophageal dehiscence connected with the esophageal purse-string, use either purse-string devices or alternative methods such as a second handsewn purse-string, U stitches of the esophagus, etc. We think that the risk of improper anastomoses after esophageal resection can be reduced if the need for the esophageal purse-string can be eliminated. This work shows our personal technique for performing esophagoenterostomy, especially in the thoracic area, using the new CEEA stapler (Autosuture) without esophageal purse-string sutures. According to the modified procedure the stapler anvil and the mini rod are introduced in the esophagectomy and a 2-0 thread is knotted around the CEEA mini rod. Then the esophageal mutilated part is closed by a linear stapler keeping a syringe needle, which contains the thread, through the linear suture. Then, using the thread as a pulling system, the surgeon makes the needle and the tip of the mini rod slide out of the esophageal suture. Now the surgeon can reassemble the CEEA and perform the anastomosis. There are many clinical reports that cite no leaks following circular stapled anastomoses across linear stapled closures.

Anastomosis, Surgical↗